the same for gnome-www-browser. So it would seem that Chrome should be the default browser? But the problem is, when I click a link in a Geary mail, Firefox opens. So somehow Firefox is also a preferred browser?!

No, I tested to write a http link in the Terminal and when using the Terminals "Open link" command it also opened in Firefox... it seems like web links in general are handled by Firefox instead of the "real" preferred Chrome application.
– Bengt OlssonOct 12 '16 at 19:17

Thanks, but I've already done all xdg-settings steps and they works as they should. I also think the issue is with mimeapps.list, but I surely shouldn't need to add and change all the entries manually, there should be some configuration that sets these when making an application default?
– Bengt OlssonOct 13 '16 at 6:23